title: Homogalacturonan, KHP1, biol rep 2

city: Ljubljana

first: Urška

last: Murovec

address: Jamnikarjeva 101

institute: Biotechnical Faculty

data_processing:
fastQC, Trimmomatic v0.39, BWA tool 0.7.17-r1188, FeatureCounts 2.0.0, R 4.1.2
Assembly: SPAdes genome assembler v3.15.3
Supplementary files format and content: raw counts for each sample

organism: Xylanibacter ruminicola

source_name: Xylanibacter ruminicola KHP1

extract_protocol:
Strains were grown in liquid minimal or modified DSMZ medium 330 containing different substrates, until they reached OD value of 0.3-0.5. 1.5 mL of each triplicate was removed and immediately combined with 3 mL of RNAprotect bacteria reagent (Qiagen). RNA was purified using RNeasy Mini Kit (Qiagen) with the on-column DNase treatment. The quantity of the isolated RNA was determined using Spark 10M multifunctional microplate reader with Quant-iTTM RNA Assay Kit (Thermo Scientific).
Illumina stranded TruSeq RNA library incl bacterial ribodepletion or NEBNext Ultra Directional RNA library prep kit

tag: strain

value: liquid culture

value: Homogalacturonan


title: T47D cells, Estradiol treated 1

status: Public on May 08 2024

type: SRA

city: Laval

first: Isabelle

last: Plante

state: Québec

address: 531 boul Des prairies

department: Armand-Frappier Santé Biotechnologie

country: Canada

institute: INRS

description:
ET1
norm_counts_limmaremovebatch_estradiol

library_source: other

data_processing:
The quality of the raw reads was assessed with FASTQC v0.11.8. Reads were trimmed using Cutadapt keeping the 22 first nucleotides. Micro-RNA were quantified using MIRDEEP software. Other small RNA were quantified using COMPSRA. Results were aggregate as a matrix and used as input into DESeq2 R package for differential expression. Differential expression was performed for all comparisons within each hormone separately while controlling for batch effect in the model.
Assembly: hg38
Supplementary files format and content: Excel sheets represent normalized counts.

molecule: other

organism: Homo sapiens

source_name: Breast

extract_protocol:
mirVana miRNA isolation kit (Thermo Fisher Scientific).
libraryTruseq Small RNA

tag: tissue

value: Breast

tag: cell line

tag: treatment

value: Estradiol 10 nM,  24 hours


title: Mtb infected GID8 knockdown macrophages 4 days post infection_3

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
STAR-2.7.10b
Reads were mapped to GRCm39 and ASM19595v2 using STAR. Raw read counts were obtained from mapped reads using HTSeq count
Raw and normalised reads were analyzed using DESeq2
Assembly: mm10, ASM19595v2
Supplementary files format and content: txt files for both raw and normalized counts

molecule: total RNA

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: Bone marrow macrophages

extract_protocol:
RNA was extracted using TRIZOL, total RNA from the aqueous phase was purified using the Zymo RNA clean and concentrator kit
Barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit after ribosomal rRNA depletion using the QIAseq FastSelect pan-bacterial and H/M/R kits
Novaseq 6000 S4

tag: cell type

value: Bone marrow macrophages

tag: genotype

value: GID8 knockdown

tag: infection

value: Mtb infected - 4 days


title: CTR_208A GPC

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description: RNA-seq

data_processing:
The sequencing reads were pre-processed with fastq(Chen et al., 2018), aligned with STAR (Dobin et al., 2013) to the genome assembly GRCh38 (Flicek et al., 2014), and quantified with RSEM (Li and Dewey, 2011) using the ENSEMBL Homo sapiens version 95 annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: RawCounts
Supplementary_files_format_and_content: TPM

source_name: GPC induced from iPSC

growth_protocol: GPCs were generated from human induced pluripotent stem cells (iPSCs) using our previously described protocol (Wang et al., 2013, Windrem et al., 2017). Cells were harvested on the basis of the expression of the bipotential GPC surface marker CD140a or the astrocytic marker CD44.

extract_protocol: Glial cell populations where used in mRNA isolation by PolyA selection and mRNA sequencing analysis, utilizing the TruSeqRNA Library Prep Kit V2.

tag: disease

value: control


title: A375_siGL2-mQ_R3

city: Lyon

first: Nicolas

last: Fontrodona

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

data_processing:
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 30 -l 25 --detect_adapter_for_pe)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10 -s reverse -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

molecule: cytoplasmic RNA

growth_protocol: A375 cells were obtained from ATCC and cultured in DMEM containing all amino-acids except glutamine (Gibco, 10938025) and supplemented with 10% FBS, 2mM glutamine and penicillin-streptomycin, at 37°C and 5% CO2. Cells were passed at around 80% confluency, 3 times a week.

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
RNA samples were sent for sequencing at Novogene (rRNA depletion library preparations, sequencing on Novaseq 6000 2x150)

treatment_protocol:
Transfection : For each gene of interest (except for GL2), 2 different siRNAs targetting constitutive exons and with minimum predicted off-targets were designed and pooled together. siRNAs were ordered lyophilysed from Merck and resuspended in sterile water at 50µM, and stored at -20°C. Cells were reverse-transfected with lipofectamine RNAimax (Thermofischer 13778030) according to the manufacturer’s instructions.
24h later, medium was removed and cells washed with warm PBS and a new medium containing (MAPK inhibitors or DMSO) OR (glutamine or not) was used, and cells harvested 24h later.

value: skin melanoma

value: Q depleted medium + siGL2


title: A375_siGL2-DMSO_R2

value: DMSO + siGL2


title: Homogalacturonan, KHP1, biol rep 1

country: Slovenia


title: T47D cells, Prolactin vehicle 3

description:
VEH3
norm_counts_limmaremovebatch_prolactin

value: 4 mM hydrochloric acid


title: A375_siGL2-DMSO_R1


title: CTR_19C GPC

description: RNA-seq


title: CTR_22E GPC

description: RNA-seq


title: A375_siEPRS1-pQ_R3

value: control medium + siEPRS1


title: T47D cells, Prolactin vehicle 2

description:
VEH2
norm_counts_limmaremovebatch_prolactin


title: CTR_208C GPC

description: RNA-seq


title: Starch, KHP1, biol rep 2

value: Starch


title: CTR_19B GPC

description: RNA-seq


title: A375_siEPRS1-pQ_R2


title: CTR_208B GPC

description: RNA-seq


title: Starch, KHP1, biol rep 1


title: T47D cells, Prolactin treated 3

description:
PRL3
norm_counts_limmaremovebatch_prolactin

value: Prolactin 8.7 nM (200 ng/mL)  8 hours


title: CTR_19A GPC

description: RNA-seq


title: A375_siEPRS1-mQ_R3

value: Q depleted medium + siEPRS1


title: Pectic galactan, KHP1, biol rep 2

value: Pectic galactan


title: CTR_17D GPC

description: RNA-seq


title: T47D cells, Estradiol control 1

description:
EC1
norm_counts_limmaremovebatch_estradiol


title: T47D cells, Prolactin treated 1

description:
PRL1
norm_counts_limmaremovebatch_prolactin


title: CTR_17C GPC

description: RNA-seq


title: CTR_19D GPC

description: RNA-seq


title: Starch, KHP1, biol rep 3

value: liquid culture


title: Pectic galactan, KHP1, biol rep 1


title: CTR_17B GPC

description: RNA-seq


title: A375_siEPRS1-mQ_R1


title: T47D cells, Prolactin control 3

description:
CTRL3
norm_counts_limmaremovebatch_prolactin


title: Arabinogalactan, KHP1, biol rep 3

value: Arabinogalactan


title: CTR_17A GPC

description: RNA-seq


title: T47D cells, Prolactin vehicle 1

description:
VEH1
norm_counts_limmaremovebatch_prolactin

value: Breast


title: A375_siEPRS1-pQ_R1


title: H9C2 CPPs-Exo 3

city: Guangzhou

first: Yingying

last: Xiao

state: Guangdong

address: A2-652, Guangzhou Medical University, Xinzao Road, Panyu District, Guangzhou

department: the School of Pharmaceutical Sciences

country: China

institute: Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genomes for rat or human using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Wellcome Sanger Institute mRatBN7.2
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

molecule: polyA RNA

organism: Rattus norvegicus

growth_protocol: H9C2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
H9C2 cells were digestion with trypsin, terminated with DMEM supplemented with 10% FBS, and then washed with PBS.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: H9C2 cells were treated with or without exosomes from cardiopulmonary progenitors for 48 hours.

value: cardiomyocytes

value: WT


title: Pectic galactan, KHP1, biol rep 3


title: A375_siEPRS1-MAPKi_R2

value: MAPK inhibitors + siEPRS1


title: H9C2 CPPs-Exo 2

value: exosomes from cardiopulmonary progenitors


title: T47D cells, Prolactin control 1

description:
CTRL1
norm_counts_limmaremovebatch_prolactin


title: T47D cells, Prolactin control 2

description:
CTRL2
norm_counts_limmaremovebatch_prolactin


title: A375_siEPRS1-MAPKi_R1


title: Rhamnogalactuornan, KHP1, biol rep 3

value: Rhamnogalactuornan


title: Arabinogalactan, KHP1, biol rep 1


title: FOXO1_stimulated&rest_3

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

description:
FOXO1_stimulated&rest_3
7.12_sorted.bam

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts. Processed data include raw and normalized counts CPM.

source_name: T cell

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from normal buffy coats using Ficoll centrifugation and PBMCs were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. PBMCs were activated with antihuman CD3 (30ng/ ml) and IL-2 (600 IU/ml) for 48 hours before transduction with a lentvirus encoding a second generation scFv–anti–Lewis-Y CAR (41BBz and CD3ζ). Cells were cultured at a density of 1x106/ml following the transduction process.

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

treatment_protocol: Cultured without stimulation (non-stimulated), activated with plate bound anti-idiotype-LeY (anti-CAR) antibody for 24 h (stimulated) or activated with plate bound anti-idiotype-LeY (anti-CAR) antibody for 24 h followed by 7 days recovery.

value: T cell

tag: donor

value: Healthy donor

tag: genetic modification

value: α-Lewis-Y-CAR

value: 24 h activation with plate bound anti-idiotype LeY and  7 days recovery


title: Homogalacturonan, KHP1, biol rep 3

value: Homogalacturonan


title: A375_siEPRS1-mQ_R2

value: skin melanoma


title: FOXO1_stimulated&rest_2

description:
FOXO1_stimulated&rest_2
7.11_sorted.bam


title: Rhamnogalactuornan, KHP1, biol rep 2


title: FOXO1_stimulated&rest_1

description:
FOXO1_stimulated&rest_1
7.10_sorted.bam


title: Rhamnogalactuornan, KHP1, biol rep 1


title: H9C2 CPPs-Exo 1


title: A375_siEPRS1-MAPKi_R3


title: A375_siEPRS1-DMSO_R1

value: DMSO + siEPRS1


title: A375_siEPRS1-DMSO_R2


title: FOXO1_stimulated_3

description:
FOXO1_stimulated_3
1.12_sorted.bam

value: 24 h activation with plate bound anti-idiotype LeY


title: A375_siCTU2-pQ_R3

value: control medium + siCTU2


title: H9C2 Control 1

value: control


title: FOXO1_stimulated_2

description:
FOXO1_stimulated_2
1.11_sorted.bam


title: FOXO1_stimulated_1

description:
FOXO1_stimulated_1
1.10_sorted.bam


title: Arabinan, KHP1, biol rep 2

value: liquid culture

value: Arabinan


title: Hela_TRMT1L_IP_Replicate2

city: Houston

first: Catherine

last: Denicourt

state: TX

address: 6431 Fannin St

department: Integrative Biology and Pharmacology

institute: The University of Texas HSC Houston

data_processing:
The raw fastq data were first trimmed to remove the adaptor sequence with CutAdapt. fastp was then used to remove and append the unique molecular identifier (UMI) to the read names. Reads shorter than 18 nt after trimming were discarded and the rest were aligned to the human genome (hg38) and human repetitive elements using the family-aware mapping approach developed by Van Nostrand et al. (Genome Biol., 2020, 21, 90). Peak calling was conducted using the PEAKachu peak calling tool (https://github.com/tbischler/PEAKachu) within the pipeline, with parameters set as follows: --paired_end --max_insert_size 220. The deduplication was performed using UMI-tools with the parameter --read-length.
Assembly: hg38 and human repetitive elements reference summarized by Van Nostrand et al. (Methods Mol. Biol., 2017, 1648, 177-200)
Supplementary files format and content: excel workbook file containing TRMT1L eCLIP sequencing Peaks with IP vs SMInput fold-change >= 2 and adjusted P value < 0.05.
Library strategy: eCLIP-seq

source_name: HeLa

growth_protocol: HCT116 and HeLa cells were cultured under 5% CO2 atmosphere at 37°C in high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplement with 5% fetal bovine serum (FBS) and 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
The eCLIP-sequencing pipeline was adapted from procedures described by Van Nostrand et al. (Methods Mol. Biol., 2017, 1648, 177-200). Cells were initially crosslinked with 400 mJ/cm2 UV on ice and lysed in CLIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1× protease inhibitor cocktail) for 15 min. RNA fragmentation was accomplished through sonication, followed by treatment with RNase T1 and Turbo DNase at 37°C for 5 minutes. The nuclease-treated lysate was immunoprecipitated with protein G Dynabeads pre-bound with anti-TRMT1L antibody or rabbit IgG overnight. The co-precipitated complex was washed sequentially with high salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1% NP-40,0.1% SDS, 0.5% sodium deoxycholate, 1 mM EDTA) and wash buffer (20 mM Tris-HCl pH 7.4, 0.2% Tween-20). The RNA-ends were repaired on beads by treatment with Fast-AP and T4 PNK.
The eCLIP-sequencing pipeline was adapted from procedures described by Van Nostrand et al. (Methods Mol. Biol., 2017, 1648, 177-200). The dephosphorylated RNA was ligated to a 3’ RNA adaptor (/5Phos/rArGrArUrCrGrGrArArGrArGrCrArCrArCrGrUrC/3SpC3/) by T4 RNA ligase on beads. The co-precipitated complex and the samples for SMInputs were resolved on an 8% SDS-PAGE gel and transferred to a nitrocellulose membrane for size selection. Samples ranging from the TRMT1L band to 75 kDa above on the membrane were excised, recovered, and prepared into libraries for paired-end sequencing on an Illumina Hi-Seq 4000 platform (Novogene).

value: HeLa

value: immortal human epithelial cell line

tag: eclip antibody

value: TRMT1L (A305-120A, Bethyl)


title: Arabinan, KHP1, biol rep 1


title: T47D cells, Prolactin treated 2

description:
PRL2
norm_counts_limmaremovebatch_prolactin

value: Breast

value: Prolactin 8.7 nM (200 ng/mL)  8 hours


title: Hela_TRMT1L_IP_Replicate1


title: FOXO1_non-stimulated_3

description:
FOXO1_non-stimulated_3
1.6_sorted.bam

value: T cell

value: no stimulation


title: A375_siEPRS1-DMSO_R3


title: Xylogluclan, KHP1, biol rep 3

value: Xylogluclan


title: A375_siCTU2-mQ_R3

value: Q depleted medium + siCTU2


title: Xylogluclan, KHP1, biol rep 2


title: FOXO1_non-stimulated_2

description:
FOXO1_non-stimulated_2
1.5_sorted.bam

value: Healthy donor

value: α-Lewis-Y-CAR


title: H9C2 Control 2

value: cardiomyocytes

value: WT


title: Arabinan, KHP1, biol rep 3


title: control_stimulated&rest_3

description:
control_stimulated&rest_3
7.9_sorted.bam

value: 24 h activation with plate bound anti-idiotype LeY and  7 days recovery


title: Hela_TRMT1L_Input_Replicate1


title: A375_siCTU2-mQ_R2

value: skin melanoma


title: FOXO1_non-stimulated_1

description:
FOXO1_non-stimulated_1
1.4_sorted.bam


title: Xylogluclan, KHP1, biol rep 1

value: liquid culture


title: A375_siCTU2-MAPKi_R3

value: MAPK inhibitors + siCTU2


title: HCT116_TRMT1L_IP_Replicate2

value: human colorectal carcinoma cell line


title: A375_siCTU2-mQ_R1


title: HCT116_TRMT1L_Input_Replicate2


title: Glucomannan, KHP1, biol rep 3

value: Glucomannan


title: Glucomannan, KHP1, biol rep 2


title: A375_siCTU2-pQ_R1

value: control medium + siCTU2


title: A375_siCTU2-pQ_R2


title: Glucomannan, KHP1, biol rep 1


title: HCT116_TRMT1L_IP_Replicate1

value: TRMT1L (A305-120A, Bethyl)


title: A375_siCTU2-MAPKi_R1


title: control_stimulated_3

description:
control_stimulated_3
1.9_sorted.bam

value: control

value: 24 h activation with plate bound anti-idiotype LeY


title: control_stimulated&rest_1

description:
control_stimulated&rest_1
7.7_sorted.bam

value: T cell


title: A375_siCTU2-MAPKi_R2


title: A375_siCTU2-DMSO_R3

value: DMSO + siCTU2


title: control_stimulated&rest_2

description:
control_stimulated&rest_2
7.8_sorted.bam


title: Galactomannan, KHP1, biol rep 2

value: Galactomannan


title: Hela_TRMT1L_Input_Replicate2

value: HeLa

value: immortal human epithelial cell line


title: siscramble rep1

city: Singapore

first: KAIJING

last: CHEN

address: 60 Nanyang Drive

department: school of biological science

country: Singapore

institute: Nanyang Technological University

library_source: genomic

data_processing:
These libraries are SIQHiC libraries, which encompass both human and mouse DNA.
The paired-end reads were mapped to merged hg19 and mm10 reference genome using BWA mem (0.7.17-r1188).
Subsequently, only the reads mapped to the human genome were retained for further analysis.
The mapped reads were then passed to Juicer pipeline (1.5.7) to perform chimeric reads analysis, merging, generating Hi-C matrix, loop calling using HiCCUPS, and TAD calling using Arrowhead.
Assembly: hg19
Supplementary files format and content: *_merged_nodups.txt.gz: tab-delimited text files include valid pairs for each Sample ...
Supplementary files format and content: *_30.hic: hic format files generated from Juicer and can be visualized by Juicebox

molecule: genomic DNA

growth_protocol: All the cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
One million siRNA-treated cells and four million of drug-treated K562 cells were individually fixed and subsequently mixed with fixed mouse 3T3 cells at a ratio of 4:1. The mixed cells were then used for Hi-C experiments using Arima-HiC kit (Arima Genomics) according to the manufacturer’s protocol.
Libraries were prepared using the KAPA Hyper-Prep Kit (KAPA), according to the Arima-HiC kit protocol.

treatment_protocol: CTCF siRNA knockdown was performed using ON-TARGETplus SMARTpool Human CTCF (10664) siRNA (Dharmacon L-020165-00-0005). After 48 hr incubation, cells were harvested for Hi-C. Another Hi-C experiment was performed, where K562 cells were either treated with 0.1% DMSO or 10 uM etoposide for 72 hr.

tag: siqhic restriction_enzyme

value: Arima

value: untreated


title: HCT116_TRMT1L_Input_Replicate1


title: Galactomannan, KHP1, biol rep 3


title: control_stimulated_2

description:
control_stimulated_2
1.8_sorted.bam

value: Healthy donor

value: α-Lewis-Y-CAR


title: siscramble rep2


title: A375_siCTU2-DMSO_R1

value: skin melanoma


title: control_non-stimulated_3

description:
control_non-stimulated_3
1.3_sorted.bam

value: no stimulation


title: Beta-glucan, KHP1, biol rep 3

value: liquid culture

value: Beta-glucan


title: Beta-glucan, KHP1,biol rep 2


title: Beta-glucan, KHP1, biol rep 1


title: A375_siCTU2-DMSO_R2


title: control_stimulated_1

description:
control_stimulated_1
1.7_sorted.bam


title: Galactomannan, KHP1, biol rep 1


title: siCTCF rep2

value: CTCF siRNA


title: A375_pQ-TCHX-0_R3

data_processing:
Only R1 reads were used for subsequence analysis
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 20 -3 --cut_tail_window_size 10 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA –adapter_sequence=AAAAAA)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10  -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
We prepared QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, LEX113.96) libraries from RNA following the manufacturer’s instructions. 500ng of RNA were spiked-in with 1µL of a 1:100 dilution of ERCC Spike-In Mix (ThermoFisher, 4456740) before the library preparation. Libraries were then quantified, pooled and sent for sequencing at Novogene (Novaseq 6000 2x150)

treatment_protocol:
siCTU2/siGL2 samples : For each gene of interest (except for GL2), 2 different siRNAs targetting constitutive exons and with minimum p redicted off-targets were designed and pooled together. siRNAs were ordered lyophilysed from Merck and resuspended in sterile water at 50µM, and stored at -20°C. Cells were reverse-transfected with lipofectamine RNAimax (Thermofischer 13778030) according to the manufacturer’s instructions. Culture medium was change to a fresh one the next day. Tryptolide/cycloheximid treatment began 42h after transfection.
Q depleted samples : cells were plated and the following day, medium was removed, cells washed with warm PBS and fresh medium cointaining glutamine (pQ) or not (mQ) was used. Tryptolide/cycloheximid treatment began 18h after this medium change.
Tryptolide/cycloheximid treatment :  cells were treated with tryptolide (25µM, T samples) or tryptolide (25µM) and fresh cycloheximid (100µg/ml, TCHX samples). This was prepared in 3 identical batches A B and C, and batch A was immediately harvested (T0 samples). Batches B and C were harvested 3h and 5h later (respectively T3 and T5 samples).

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 0 hours


title: siCTCF rep1


title: A375_-Q_R1

description: sequencing batch #1 - experimental batch 1

data_processing:
Adapters were removed from raw reads using cutadapt version 2.1 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -u 13 --maximum-length=40 --minimum-length=20 -q 28,28)
Reads were trimmed using UrQt version 1.0.18
Reads were mapped to GRCh38.p13 coding genes using hisat2 version 2.2.1 (parameters parameters --rna-strandness 'F' –norc).
Alignment files were converted, with deeptools version 3.0.2, to bigWig files containing CPM (count per million mapped reads) normalized coverage at one nucleotide resolution
Assembly: GRCH38.p13
Supplementary files format and content: Bigwig files containing the ribosome footprints CPM normalized coverage at one nucleotide resolution for each sample

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS  supplemented with 100µg/ml cycloheximide (Sigma, 01810). Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100) , and incubated on ice for 10 minutes. The PBS and lysis buffer were supplemented with 100µg/ml cycloheximide (Sigma, 01810) and 2mM DTT the day of use. 260nm absorbance of the lysate was measured to estimate the total quantity of material and then subjected to nuclease digestion. For 5 units of A260 absorbance, 6µl of MNase (Nuclease S7 10107921001, Roche, 1mg/ml) were added to the lysate, along with CaCl2 to a final concentration of 10mM. The tubes were then incubated at 25°C for 30 minutes and transferred on ice, and the digested lysates were then carefully laid on top of 10%-50% sucrose gradients containing cycloheximide (100µg/ml). The gradients were then ultra-centrifuged at 35,000 rpm for 2h40min at 4°C and run on a fraction collector. The fractions containing the digested monosome fragments (80S) were kept and SDS was added to a final concentration of 1%, before the digestion with proteinase K (Roche, 03115828001, final concentration of 2µg/ml) for 45min at 42°C. Protected RNA fragments were then purified using an acidic phenol-chloroform extraction (Fischer, BP1753I) and precipitated overnight at -20°C with 0.1x volume of  sodium acetate (3 M, pH 5.2), 1x vol isopropanol, 1µl GlycoBlue and 10mM MgCl2 (use 10mM MgCl2 at every precipitation step, helps to recover smaller nucleic acids). Purified RNA fragments were then 3’-end dephosphorylated using PNK and run on a 10% acrylamide denaturing gel, and smears of interest (26-32bp) were cut from the gel and purified. Size-selected fragments were then rRNA-depleted by hybridization using RNA probes, and successively RNAse H and DNAse-treated, and purified with a new phenol-chloroform extraction before the Omniprep Library preparation.
Ribosome profiling Omniprep libraries were sequenced by GenomEast (Hiseq 4000 1x50bp).

treatment_protocol: For the glutamine depletion experiment, the medium was not supplemented with glutamine. For  the MAPK inhibitors treatment , cells were plated and the following day, the culture medium was removed and replaced with fresh medium containing vemurafenib and cobimetinib.  Cells were treated for 24h at 1µM (500nM vemurafenib + 500nM cobimetinib).

value: Q depleted medium for 24h


title: Pullulan, KHP1, biol rep 3

value: Pullulan


title: TCF7_non-stimulated_3

treatment_protocol: Cultured without stimulation (non-stimulated)

value: T cell


title: H9C2 Control 3

value: cardiomyocytes

value: WT

value: control


title: A375_pQ-T-3_R3

value: cells grown in a control medium followed by tryptolide treatment for 3 hours


title: TCF7_non-stimulated_1


title: Pullulan, KHP1, biol rep 1


title: A375_CTRL_R2

description: sequencing batch #1 - experimental batch 2

value: control medium for 24h


title: A375_pQ-T-0_R3

value: cells grown in a control medium followed by tryptolide treatment for 0 hours


title: A375_pQ-TCHX-5_R3

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 5 hours


title: FOXO1_non-stimulated_3

value: Healthy donor

value: α-Lewis-Y-CAR


title: control_non-stimulated_2

description:
control_non-stimulated_2
1.2_sorted.bam

value: no stimulation


title: A375_pQ-TCHX-3_R3

value: skin melanoma

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 3 hours


title: A375_-Q_R3


title: Glucose, KHP1, biol rep 3

value: liquid culture

value: Glucose


title: control_non-stimulated_1

description:
control_non-stimulated_1
1.1_sorted.bam


title: TCF7_non-stimulated_2


title: A375_CTRL_R1


title: A375_pQ-T-5_R3

value: cells grown in a control medium followed by tryptolide treatment for 5 hours


title: Glucose, KHP1, biol rep 2


title: Pullulan, KHP1, biol rep 2

value: Pullulan


title: FOXO1_non-stimulated_1

value: T cell


title: control_non-stimulated_3


title: A375_pQ-TCHX-0_R2

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 0 hours


title: A375_DMSO_R2

description: sequencing batch #2

value: DMSO for 24h


title: Arabinogalactan, KHP1, biol rep 2

value: Arabinogalactan


title: A375_CTRL_R3


title: A375_pQ-TCHX-5_R2


title: FOXO1_non-stimulated_2


title: control_non-stimulated_2

value: control


title: A375_DMSO_R3

description: sequencing batch #2


title: A375_-Q_R2

value: Q depleted medium for 24h


title: A375_MAPKi_R3

description: sequencing batch #2

value: MAPK inhibitors for 24h


title: Caulobacter_early_stationary_R3

city: Rehovot

first: Jens

last: Hör

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute for Science

data_processing:
Demultiplexing using bcl-convert v4.2.4
Trimming using Trim Galore v0.6.7 with default parameters
Mapping using BBMap v39.06 with default parameters
Read counting using featureCounts v2.0.3 with -s 1
Assembly: GCF_001425745.1, NC_000913.3
Supplementary files format and content: Excel file containing TPM values for each sample

organism: Caulobacter sp. Root343

extract_protocol:
E. coli expressing the Bil system under control of a tetracycline-inducible promoter was grown to mid-log phase with 25 ng/ml aTc as inducer. Caulobacter sp. Root343 was grown to mid-log, late-log or early stationary phase. Samples corresponding to an OD600 of 2 were taken and immediately mixed with ¼ volume of stop mix (95% ethanol, 5% saturated phenol) and frozen in liquid nitrogen. The samples were then thawed on iced followed by centrifugation at 4,000 g and 4°C for 10 min. The supernatant was discarded and the cell pellets resuspended in 1 ml of TRIzol (Thermo Scientific) followed by RNA extraction according to the manufacturer’s protocol. The resulting RNA pellet was dissolved in 40 µl of water. To get rid of contaminating DNA, 0.5 µl of water, 5 µl DNase I buffer with MgCl2 (Thermo Scientific), 0.5 µl of RNase inhibitor (Thermo Scientific) and 4 µl DNase I (Thermo Scientific) was added and the mixture incubated at 37°C for 30 min. The DNase-digested RNA was subjected to acidic phenol-chloroform extraction and finally dissolved in 30 µl of water.
Extracted RNA was depleted of ribosomal RNA using a commercial rRNA depletion kit for mixed bacterial samples (Lexogen, RiboCop META, #125). The depleted RNA samples were fragmented using ultrasound (2 pulses of 30 s at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase with the 3’ adapter as primer. After purification, the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified using a high-fidelity DNA polymerase and the barcoded TruSeq-libraries were pooled in approximately equimolar amounts. Sequencing of pooled libraries, spiked with PhiX control library, was performed at a minimum of 10 million reads per sample in single-ended mode with 100 cycles on the NextSeq 2000 platform (Illumina).

tag: phase

value: early stationary


title: A375_pQ-TCHX-3_R2


title: A375_pQ-T-0_R2

value: cells grown in a control medium followed by tryptolide treatment for 0 hours


title: Glucose, KHP1, biol rep 1


title: pbmc,42c_TCR

city: Hannover

first: Ximena

last: Leon Lara

state: Please select a region.

address: Carl-Neuberg-Strasse 1

country: Germany

institute: Hannover Medical School

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v3.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: pbmc

extract_protocol:
Thawed PBMC were rested for 1hour in RPMI 1640 supplemented medium. Different time points per donor were labeled with different TotalSeq anti-human hashtag antibodies.
Single-cell transcriptome sequencing and scTCR-seq were performed on FACS sorted gamma-delta T cells and B cells using the Chromium Single-Cell 5′ Library Gel Bead and Construction Kit and the Chromium Single-Cell V(D)J Enrichment Kit according to the user guidelines.
scRNA-seq, scTCR-seq, Cell surface protein library.

value: pbmc


title: Caulobacter_early_stationary_R1


title: A375_pQ-TCHX-5_R1

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 5 hours


title: pbmc,42b_TCR


title: A375_pQ-T-5_R2

value: skin melanoma


title: A375_DMSO_R1

description: sequencing batch #2


title: Caulobacter_early_stationary_R2


title: RNAseq EV rep2

data_processing:
For the RNA-seq reads of K562 EV, S1KO, S2KO and DKO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For the RNA-seq reads of K562 DMSO, X5050, GSK343, combined 8H, combined 24H and combined 72H, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using STAR (2.7.3a) with parameters ”--runThreadN 16 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts --readFilesCommand zcat --twopassMode Basic --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --chimSegmentMin 20 --chimJunctionOverhangMin 20 --chimOutJunctionFormat 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentReadGapMax 0 --alignSJstitchMismatchNmax 0 -1 0 0 ”. Differentially expressed genes were called using Deseq2(0.29.0) .
Genome_build: hg19
Supplementary_files_format_and_content: *.tsv : *.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
Supplementary_files_format_and_content: *.tab: *.tab is a plaintext file of the abundance estimates generated by STAR with --quantMode GeneCounts option. Fields contained: 1. gene id ; 2. counts for unstranded RNA-seq; 3. counts for the 1st read strand aligned with RNA; 4. counts for the 2nd read strand aligned with RNA.

source_name: K562 cells with empty vector

extract_protocol:
Total RNA were isolated from the cells using RNeasy Mini Kit (Qiagen) together with performing on-column DNase digestion (Qiagen). RNA concentrations were determined by Nanodrop ND1000 (Thermo Scientific).
The quality of the RNA extracted was analyzed using Agilent RNA 6000 Nano Kit (Agilent), and quantitated using Nanodrop ND1000 (Thermo Scientific). Library construction was performed using TruSeq Stranded Total RNA LT (w/ Ribo-Zero Gold) Set A (Illumina) as per protocol.

treatment_protocol: EV, S1KO, S2KO and DKO cells undergoes the CRISPR excision. The drug treated K562 cells were either treated with DMSO-72h, 5uM GSK343-72h, 100uM X5050-72h or combinational treatment (5uM GSK343+100uM X5050-72h). The time course GR treatment was done for either 8h or 24h treatment of the same concentration of GR as 72h.

value: untreated


title: A375_pQ-T-3_R2

value: cells grown in a control medium followed by tryptolide treatment for 3 hours


title: Caulobacter_late_log_R1

value: late log


title: RNAseq EV rep1


title: control_non-stimulated_1

value: Healthy donor

value: α-Lewis-Y-CAR

value: no stimulation


title: A375_MAPKi_R2

description: sequencing batch #2


title: Caulobacter_mid_log_R3

value: mid log


title: Caulobacter_mid_log_R2


title: pbmc,41b_TCR


title: Caulobacter_late_log_R2


title: A375_pQ-TCHX-3_R1

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 3 hours


title: pbmc,41d_TCR


title: A375_mQ-TCHX-5_R3

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 5 hours


title: RNAseq S1KO rep1

source_name: K562 cells with silencer1 KO

value: knockout silencer1 region


title: Caulobacter_late_log_R3


title: A375_MAPKi_R1

description: sequencing batch #2


title: RNAseq DKO rep2

source_name: K562 cells with silencer1 and silencer2 DKO

value: knockout silencer1 and 2 regions


title: Single cell, Hippocampus, Metll3CKOE-Mut

city: Beijing

first: Magdalena

middle: Justyna

last: Koziol

address: Science Park Road

institute: Chinese Institute for Brain Researach, CIBR

description: BDTM Rhapsody docker setup (BD)

library_source: transcriptomic single cell

data_processing:
For single cell RNA-seq and m6A identification: Filtered barcode matrices obtained from E-YTH and E-YTHmut single cell data were processed by Seurat. Specifically, we excluded cells exhibiting Mettl3 transcript counts equal to or exceeding 1, in pursuit of heightened stringency.The software Bullseye was used to identify m6A sites in single cell sequencing data (Tegowski et al., 2022) without considering those sites within Mettl3-expressing cells.
For single cell RNA-seq matrix files were generated
cims files were generated
Assembly: m39
Supplementary files format and content: For single cell RNA-seq: matrix files

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice: Hippocampi were harvested from adult mice(8-12weeks). Animals were maintained and processed in accordance with CIBR guidelines. All experimental methods were approved and followed all regulations of the Welfare and Ethics Review Committee for Laboratory Animals.  Mettl3-floxed mice, which were originally purchase from GemPharmatech Co.,Ltd, were crossed with the Emx1-Cre (The Jackson Laboratory;#005628)(Gorski et al. 2002), whose progeny with hemi deletion of Mettl3 (Mettl3+/−:Emx1-Cre) mated with Mettl3fl/fl mice to maintain the colonies and subsequently the mice (Mettl3+/−:Emx1-Cre) were used for single cell RNA sequencing.

extract_protocol:
For mouse hippocamus collections, hippocampi were dissected 2 weeks after AAV injectsions; for single cell analysis, cells were dissociated 2 weeks after AAV injections with using the Adult Brain Dissociation Kit (Miltenyi Biotex no. 130-107-677);
For single cell sequencing: Briefly, after hippocampi dissociation, cells were FACS sorted and live cells were collected in ice-cold PBS containing 0.5% BSA. Per sample, 30,000 cells were loaded into a Rhapsody Cartridge (BD) and processed following the manufacturer’s instructions. Subsequently, single cell RNA sequencing libraries were prepared using the Rhapsody WTA kit (BD).
for single cells: Rhapsody WTA kit (BD)

treatment_protocol: Stereotaxic injections were performed on mice with AAV viruses followed by an additional injection into the retro-bulbar sinus.

value: hippocampus

value: C57BL/6J  Mettl3-EMX1-cre

value: E-Mut expressed


title: pbmc,41b_GEX_GD

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v3.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

value: pbmc

tag: cell type (facs-sorted)

value: gamma-delta T cells


title: A375_pQ-TCHX-0_R1

value: skin melanoma

value: cells grown in a control medium followed by cycloheximid and tryptolide treatment for 0 hours


title: pbmc,41c_TCR


title: RNAseq DKO rep1


title: pbmc,41c_GEX_GD_B

value: gamma-delta T cells and B cells


title: A375_mQ-TCHX-3_R3

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 3 hours


title: RNAseq X5050 rep2

source_name: K562 cells with X5050

value: treated with 100µmX5050 for  72hours


title: RNAseq S2KO rep2

source_name: K562 cells with silencer2 KO

value: knockout silencer2 region


title: A375_mQ-T-5_R3

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 5 hours


title: pbmc,19d_TCR


title: RNAseq X5050 rep1


title: pbmc,19c_TCR


title: TumorCell_GFP+_d10-1

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

state: CA

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

data_processing:
Reads were mapped to the mm10 genome assembly using Tophat (ver 2.1.1).
Reads within genes were counted for exon or intron regions using HTSeq (1.99.2).
Differentially expressed genes were called with DESeq2.
Assembly: mm10
Supplementary files format and content: ExonCountsDESeq2.txt, tab-delimited text file of normalized counts and DESeq2 output.
Supplementary files format and content: IntronicCountsDESeq2.txt, , tab-delimited text file of normalized counts and DESeq2 output.

source_name: Lung

extract_protocol:
RNA was treated with DNaseI(Qiagen) and isolated with the RNeasy Micro Kit (Qiagen)
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

treatment_protocol: Sorted tumor cells (Dead-/CD45-/ Epcam+/GFP+) were isolated in three biological replicates from different animals infected with Con or mA1 dRNAs after 16 weeks post tumor initiation (pti).

value: Lung

value: lung adenocarcinoma. Dead-/CD45-/ Epcam+/GFP+)

value: K-rasG12D+,p53-/-,Cas9+GFP+,mA1 dRNA

value: mA1 dRNA


title: A375_pQ-T-5_R1

value: cells grown in a control medium followed by tryptolide treatment for 5 hours


title: TumorCell_GFP+_dTom3

value: K-rasG12D+,p53-/-,Cas9+GFP+,Con dRNA

value: Con dRNA


title: A375_pQ-T-3_R1

value: cells grown in a control medium followed by tryptolide treatment for 3 hours


title: pbmc,19b_TCR

value: pbmc


title: pbmc,19a_TCR


title: Caulobacter_mid_log_R1

value: mid log


title: RNAseq S1KO rep2

value: knockout silencer1 region


title: A375_pQ-T-0_R1

value: skin melanoma

value: cells grown in a control medium followed by tryptolide treatment for 0 hours


title: RNAseq combined 72H rep1

source_name: K562 cells with combination of GSK343 and X5050 for 72h

value: treated with GSK343 and X5050 for 72 hours


title: RNAseq DMSO rep2

source_name: K562 cells with DMSO

value: untreated


title: Single cell, Hippocampus, Metll3CKOE-YTH

description: BDTM Rhapsody docker setup (BD)

value: hippocampus

value: C57BL/6J  Mettl3-EMX1-cre

value: E-YTH expressed


title: pbmc,41d_GEX_GD_B

value: gamma-delta T cells and B cells


title: A375_mQ-T-5_R2

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 5 hours


title: TumorCell_GFP+_dTom1

value: Lung

value: lung adenocarcinoma. Dead-/CD45-/ Epcam+/GFP+)


title: pbmc,42b_GEX_GD

value: gamma-delta T cells


title: pbmc,18b_TCR


title: TumorCell_GFP+_d10-3

value: K-rasG12D+,p53-/-,Cas9+GFP+,mA1 dRNA

value: mA1 dRNA


title: RNAseq DMSO rep1


title: A375_mQ-TCHX-0_R3

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 0 hours


title: RNAseq S2KO rep1

value: knockout silencer2 region


title: pbmc,42c_GEX_GD

value: pbmc


title: TumorCell_GFP+_d10-2


title: NMX_AM, scRNAseq

city: San Francisco

first: Rahul

last: Kumar

address: 1001 Potrero Ave, Rm.5K1

department: Medicine

institute: University of California, San Francisco, USA

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39  v.104
Supplementary files format and content: Tab-separated values files (Combined) unfilterd raw read counts and normalized filterd read counts

extract_protocol:
Freshly collected alveolar macrophge from Cx3cr1+/GFP reporter mice used for single cell RNA sequence.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Alveolar Macrophage

value: C57BL/6J Cx3Cr1/-

tag: age

value: 6-8 weeks old

value: unexposed


title: A375_mQ-T-0_R2

value: skin melanoma

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 0 hours


title: 4C EV rep2

data_processing:
Library strategy: 4C-seq
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include interactions information from 4C-seq by r3cSeq

extract_protocol:
40 million cells were cross-linked with 1% formaldehyde. The nuclei pellets were isolated by cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 5mM EDTA, 0.5% NP 40) supplemented with protease inhibitors (Roche). The first digestion was performed overnight at 37°C with HindIII enzyme (NEB). Digestion efficiency was measured by gel electrophoresis. After confirmation of good digestion efficiency, DNA was ligated overnight at 16°C by T4 DNA ligase (Thermo Scientific) and de-crosslinked by proteinase k. After that, DNA was extracted by phenol-chloroform and this DNA was referred as “3C library”. The “3C library” was then processed for second digestion with DpnII enzyme (NEB) overnight at 37°C. After ligation, we obtained “4C template DNA. The concentration of the 4C DNA was determined by Qubit assays (Thermo Scientific).
The 4C template DNA was then amplified using specific primers with Illumina Nextera adapters and sent for sequencing on the MiSeq platform.

treatment_protocol: EV, S1KO and DKO cells undergoes the CRISPR excision.

tag: 4c restriction enzyme

value: HindIII, DpnII

value: untreated


title: pbmc,19c_GEX_GD_B

value: gamma-delta T cells and B cells


title: 4C EV rep1


title: A375_mQ-T-3_R3

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 3 hours


title: A375_mQ-TCHX-3_R1

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 3 hours


title: mT4 cells treated with RT and anti-PD-L1, scRNAseq

city: Ann Arbor

first: Meredith

last: Morgan

state: Michigan

address: 1301 Catherin St

department: Radiation Oncology

institute: University of Michigan

description: 10x Genomics

data_processing:
Bcl2fastq2 Conversion Software for generating de-mulitplexed fastq files
CellRanger v7 Pipeline for read alignment and count matrices
Assembly: mm10
Supplementary files format and content: tab-seperated values files and matrix files

source_name: pancreatic tumor

growth_protocol: mT4 cells were grown in DMEM culture media with 10% fetal bovine serum. Cells were washed with PBS and trypsinized. Cells were collected and diluted to a concentration of 10 million cells/ml. 1 million cells were subcutaneously injected into 6-8 week old C57/Bl6 mice in 100ul injections.

extract_protocol:
6-8 tumors per treatment group were harvested, minced and digested in collagenase digest buffer (RPMI, Type I collagenase 0.1mg/ml, Type IV collagenase 0.1mg/ml, Dnase 2ul/ml) for 30 minutes at 37°C. Tissue digest was filtered using a 40um mesh filter and was quenched by washing with 2% FBS in PBS. Cells were counted and depleted of dying cells twice using the Dead Cell Removal kit from Miltenyi per manufacturer protocol. CD45 isolation kit from Miltenyi was used to seperate CD45- and CD45+ cells. Equal amounts of CD45- and CD45+ cells were mixed together in single cell suspension and counted once more. Samples were diluted to a final concentration of 700-1000cells/ul. Samples with greater then 85% viability were processed for sequencing. Single cell RNA-sequencing was performed at the University of Michigan Advanced Genomics Core Research Facility.
Single-cell 3' library generation was performed on the 10x Genomics Chromium Controller following the manufacturers protocol for the 3' v3.1 chemistry with NextGEM Chip G reagents (10x Genomics, Pleasanton, CA, USA). Library qualtiy was assessed by LabChip GXII HT (PerkinElmer) and wuantified by Qubit (Thermo Fisher Scientific).

treatment_protocol: Mice were treated with AZD1390 (20mg/kg) for 5 days starting on day 0, 1 dose of radiation (8Gy) on day 0, and 3 doses of anti-PD-L1 (100ug) once every three days starting on day -1. 6-8 tumors per treatment group were harvested on day 5.

value: pancreatic tumor

value: epithelial

value: 6-8 weeks

tag: Sex

value: female


title: RNAseq GSK343 rep2

source_name: K562 cells with GSK343

value: treated with 5µmGSK343 for 72hours


title: A375_mQ-T-0_R3


title: RNAseq GSK343 rep1


title: TumorCell_GFP+_dTom2

value: Lung

value: lung adenocarcinoma. Dead-/CD45-/ Epcam+/GFP+)

value: K-rasG12D+,p53-/-,Cas9+GFP+,Con dRNA

value: Con dRNA


title: mT4 cells treated with AZD1390, scRNAseq

description: 10x Genomics

tag: strain


title: A375_mQ-TCHX-0_R1

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 0 hours


title: A375_mQ-TCHX-5_R2

value: skin melanoma

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 5 hours


title: A375_mQ-TCHX-3_R2


title: RNAseq combined 72H rep2

value: treated with GSK343 and X5050 for 72 hours


title: mT4 cells treated with IgG control, scRNAseq

description: 10x Genomics

tag: tissue

value: Control


title: pbmc,18d_TCR

value: pbmc


title: 7D_IP_IV_IM, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39  v.104
Supplementary files format and content: Tab-separated values files (Combined) unfilterd raw read counts and normalized filtered read counts

extract_protocol:
Freshly collected interstitial macrophage from Cx3cr1+/GFP reporter mice used for single cell RNA sequence.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Interstitial Macrophage

value: C57BL/6J Cx3Cr1/-

value: 6-8 weeks old

value: Schistosoma IV challenge

tag: time


title: pbmc,18d_GEX_GD_B

value: gamma-delta T cells and B cells


title: 7D_IP_IV_AM, scRNAseq

description: 10x Genomics

value: Alveolar Macrophage

tag: treatment

value: 7 day post  Schistosoma IV challenge


title: pbmc,18c_TCR


title: A375_mQ-TCHX-0_R2

tag: cell line

tag: cell type


title: 3D_IP_IV_AM, scRNAseq

description: 10x Genomics

value: Lung

value: 3 day post  Schistosoma IV challenge


title: A375_mQ-T-0_R1

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 0 hours


title: A375_GL2-TCHX-5_R3

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 5 hours


title: 1DIP_IV_AM, scRNAseq

description: 10x Genomics

value: 1 day post  Schistosoma IV challenge


title: pbmc,18a_GEX_GD_B


title: DKO input DNA rep2

data_processing:
ChIP-seq reads of H3K27me3, H3K27ac from EV, S1KO and DKO cells were mapped by BOWTIE2(v2.2.5) using default parameters in pair-end mode. We filtered out alignments with mapq scores smaller than 30. The two replicates were combined and peaks and bigWig files were generated by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
Genome_build: hg19
Supplementary_files_format_and_content: *.narrowPeak
Supplementary_files_format_and_content: *.broadPeak

extract_protocol:
Cells were fixed with 1% formaldehyde (Thermo Scientific) at room temperature for 10 min, followed by quenching with glycine for 5 min at room temperature. The fixed cell pellets were lysed in 1% SDS lysis buffer supplemented with protease inhibitor cocktail tablet (Roche), and sonicated using Bioruptor (Diagenode). The cell lysate was precleared through centrifuging in dilution buffer and incubating with Protein G Dynabeads (Invitrogen) overnight at 4 °C. The precleared lysate was added into the antibody-conjugated beads, and incubated overnight at 4 °C, with rotation. The incubated beads were then washed thrice by 0.1% SDS lysis buffer, once by high salt wash buffer, once by lithium chloride wash and once by the TE buffer. After washing, the incubated beads were added into the elution buffer with RNase A (Qiagen) followed by decrosslinking with Proteinase K (Ambion) at 37 °C overnight. ChIP DNA was extracted back by using the QIAquick PCR purification kit (Qiagen), and quantitated using Qubit High Sensitivity dsDNA Assay (Invitrogen).
ChIP-seq library construction was prepared by using ThruPLEX DNA-seq 48D Kit (Rubicon) according to the instruction.

tag: chip antibody

value: knockout silencer1 and 2 regions


title: pbmc,40,bcd#tcr

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v3.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq


title: DKO H3K27ac rep2

value: H3K27ac (ab4729, Abcam)


title: A375_mQ-T-3_R2

value: skin melanoma

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 3 hours


title: pbmc,39,abcd#tcr

value: pbmc


title: pbmc,18a_TCR


title: K562 H3K27me3 HiChIP

data_processing:
Library strategy: HiChIP
HiChip analysis was done by following the documentation of Dovetail (https://hichip.readthedocs.io/en/latest/index.html) step by step. Paired-end reads were aligned to hg19 using BWA mem (0.7.17-r1188) with parameter “-5SP -T0” to get mapped reads in sam file format. Next, the mapped reads were processed by pairtools (0.3.0) to perform valid ligation recording, sorting, removing PCR duplicates, and splitting. After this step, pairs and bam were obtained from pairtools. Bam file was then sorted and produced index file using samtools for downstream analysis. Before the further process, the quality of HiChip library and the enrichment of HiChIP reads at H3K27me3 binding sites were evaluated by the QC report generated from get_qc.py and enrichment_stats.sh scripts in HiChIP.
After Pasing the QC assessment, pairs file from pairtools was converted into contact matrix in hic format by Juicer Tools and HiChip loops were called by FitHiChIP (9.0) in 25kb bin size.
Genome_build: hg19
Supplementary_files_format_and_content: *.bed
Supplementary_files_format_and_content: *.hic

source_name: K562 wild type cells

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
Five million cells was fixed and used for HiChIP experiment using Dovetail HiChIP MNase kit (Dovetail Genomics) according to the manufacturer’s protocol. Briefly, 1ul MNase enzyme mix and 1250ng H3K27me3 antibody were used for HiChIP experiment.
Libraries were prepared using the Dovetail Primer Set for Illumina and Dovetail Library Module for Illumina kits, according to the manufacturer’s protocol.

tag: hichip antibody

value: H3K27me3 (C36B11, Cell Signaling Technologies)

value: untreated


title: pbmc,19d_GEX_GD_B


title: mT4 cells treated with AZD1390, RT and anti-PD-L1, scRNAseq

description: 10x Genomics

value: pancreatic tumor

value: epithelial

value: 6-8 weeks

value: female


title: pbmc,19b_GEX_GD_B

value: gamma-delta T cells and B cells


title: A375_GL2-T-5_R3

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 5 hours


title: 4C S1KO rep2

value: HindIII, DpnII

value: knockout silencer1 region


title: Wildtype control, twenty week old lens 3

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

data_processing:
Raw reads were quality-analyzed using FastQC and MultiQC .
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cut adapt and trim galore with paramaters  -q 20 --phred33 --length 20.
Trimmed sequence reads were mapped to GrCM39 using Hisat2 incorporating splice juncation from genecode GTF .
Gene counts were generated using Stringtie2.1.5. For microRNA-sequencing, bowtie (version1.3.1) was used for alignment followed by mirdeep2 (0.1.2) and the miRbase release 22.1
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: Normalized gene count matrix from DESeq2 mRNAs. Count file for miRNA.

source_name: Lens

extract_protocol:
For miRNA-sequencing: Total RNA was extracted using mirVanaTM miRNA isolation kit (# AM1560, ThermoFisher Scientific). Small RNA was isolated from total RNA by size-selection and NEBNext Multiplex Small RNA Library Prep Kit was used for 50bp-single-ended sequencing. For mRNA sequencing Total RNA was extracted using the RNEasy Mini Kit (Qiagen cat. 74104) following the manufacturer’s instructions.
For miRNA libraries were prepared in Genomics and Sequencing core, University of Cincinnati using NEBNext Multiplex Small RNA Library Prep Kit. For mRNA sequencing RNA libraries were constructed by Novogene (Sacramento, CA, USA) using a TruSeq (Illumina) library prep kit.

value: Lens

tag: genotype

value: FVB/N


title: A375_mQ-TCHX-5_R1

value: cells grown in a Q depleted medium for 18h followed by cycloheximid and tryptolide treatment for 5 hours


title: pbmc,19a_GEX_GD_B


title: Wildtype control, twenty week old lens 1


title: 4C S1KO rep1


title: A375_GL2-T-3_R3

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 3 hours


title: miR26 Knockout without cataract , twenty weeks old lens 3

value: miR26 knockout in FVB/N background


title: A375_mQ-T-5_R1

value: skin melanoma

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 5 hours


title: 4C DKO rep2

value: knockout silencer1 and 2 regions


title: A375_mQ-T-3_R1

value: cells grown in a Q depleted medium for 18h followed by tryptolide treatment for 3 hours


title: pbmc,40,bcd#

value: pbmc


title: pbmc,18c_GEX_GD_B


title: EV H3K27me3 rep2

value: H3K27me3 (C36B11, Cell Signaling Technologies)

value: untreated


title: A375_GL2-TCHX-5_R2

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 5 hours


title: 4C DKO rep1


title: 3D_IP_IV_IM, scRNAseq

description: 10x Genomics

value: Interstitial Macrophage

value: Lung

value: C57BL/6J Cx3Cr1/-

value: 6-8 weeks old

value: Schistosoma IV challenge


title: 1D_IP_IV_IM, scRNAseq

description: 10x Genomics


title: EV H3K27ac rep2

value: H3K27ac (ab4729, Abcam)


title: DKO H3K27me3 rep2


title: NMX_IM, scRNAseq

description: 10x Genomics

value: control


title: A375_GL2-TCHX-0_R3

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 0 hours


title: A375_GL2-TCHX-3_R3

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 3 hours


title: LAD 3

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to the GRCm38.M23 version of the Mus musculus genome using STAR v2.7.3a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 3 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.01 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a customized Gencode GRCh38 v32 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCh38 v32
Supplementary files format and content: RawCountFile.txt Raw counts expression matrix.
Supplementary files format and content: RawCountFile_filtered.txt Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: CPM_TMM_counts.txt TMM-normalized Counts Per Million expression matrix.

source_name: gingiva tissues

extract_protocol:
Human gingival tissues were placed in Miltenyi M tubes (Miltenyi Biotec, 130-096-335) containing 1ml of Trizol reagent (Life Technologies, 15596018). Tubes were placed in Miltenyi gentlemacs and RNA 02.01 program was run. Samples were removed from M tube, placed in a 1.5 ml RNA-DNA free tube, and continue with Trizol RNA isolation protocol.”
Library preparation was performed according to the manufacturer’s instructions for the NEBNext Ultra Directional kit. The libraries were then pooled and sequenced using 75bp single end red mode on a NextSeq 500 sequencer (Illumina).

value: gingiva tissues

tag: disease


title: miR26 Knockout with cataract , twenty weeks old lens 1

value: Lens

value: miR26 knockout in FVB/N background


title: pbmc,18b_GEX_GD_B

value: gamma-delta T cells and B cells


title: A375_GL2-T-3_R2

data_processing:
Only R1 reads were used for subsequence analysis
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 20 -3 --cut_tail_window_size 10 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA –adapter_sequence=AAAAAA)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10  -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

value: skin melanoma

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 3 hours


title: DKO H3K27me3 rep1

value: H3K27me3 (C36B11, Cell Signaling Technologies)

value: knockout silencer1 and 2 regions


title: Wildtype control, twenty week old lens 2

value: FVB/N


title: DKO input DNA rep1


title: pbmc,39,abcd#sur

value: pbmc


title: pbmc,40,bcd#sur


title: LAD 2


title: DKO H3K27ac rep1


title: A375_GL2-T-0_R3

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 0 hours


title: miR26 Knockout without cataract , twenty weeks old lens 2


title: pbmc,39,abcd#


title: EV input DNA rep2

value: untreated


title: miR26 Knockout without cataract , twenty weeks old lens 1


title: EV H3K27ac rep1


title: A375_GL2-TCHX-3_R2


title: S1KO H3K27me3 rep2

value: knockout silencer1 region


title: Perio 8

value: chronic pariodontiits


title: LAD 4


title: A375_GL2-TCHX-0_R2


title: EV H3K27me3 rep1


title: miR26 Knockout , five days old lens 1


title: miR26 Knockout with cataract , twenty weeks old lens 2


title: A375_GL2-TCHX-3_R1


title: S1KO input DNA rep2


title: EV input DNA rep1


title: Wildtype control, five days old lens 3


title: Perio 6


title: LAD 5


title: miR26 Knockout with cataract , twenty weeks old lens 3


title: miR26 Knockout , five days old lens 3


title: A375_GL2-T-5_R2

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 5 hours


title: LAD 1


title: A375_GL2-T-0_R2


title: A375_GL2-T-5_R1


title: Wildtype control, five days old lens 1


title: Perio 5


title: miR26 Knockout , five days old lens 2


title: A375_GL2-TCHX-5_R1

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 5 hours


title: A375_GL2-T-0_R1


title: DKO rep2

description:
DKO_merged_nodups.txt.gz
DKO_inter_30.hic

data_processing:
The two replicates were combined and paired-end reads are mapped separated using BWA mem (0.7.17-r1188) to hg19 reference genome. The mapped reads are then passed to Juicer pipeline (1.5.7) to perform chimeric reads analysis, merging, generating Hi-C matrix, loop calling using HiCCUPS, and TAD calling using Arrowhead.
Genome_build: hg19
Supplementary_files_format_and_content: *_merged_nodups.txt.gz: tab-delimited text files include valid pairs for each Sample
Supplementary_files_format_and_content: *_30.hic: hic format files generated from Juicer and can be visualized by Juicebox

extract_protocol:
One million cells was fixed and used for HiC experiment using Arima-HiC kit (Arima Genomics) according to the manufacturer’s protocol.
Libraries were prepared using the KAPA Hyper-Prep Kit (KAPA), according to the Arima-HiC kit protocol.

tag: hic restriction enzyme

value: Arima


title: Perio 7

value: gingiva tissues


title: S1KO H3K27ac rep2

value: H3K27ac (ab4729, Abcam)


title: A375_CTU2-TCHX-3_R3

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 3 hours


title: S1KO input DNA rep1


title: S1KO H3K27me3 rep1


title: ABCT_Buffer_3

city: Shanghai

first: Qiaoying

last: Lv

address: No. 419, Fangxie Road

institute: Obstetrics & Gynecology Hospital of Fudan University

data_processing:
Skewer (v0.2.2) and FastQC (v0.11.5).
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2.
The read length was 2×150 bp.
Assembly: StringTie v1.3.1c
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample.

source_name: spleen

extract_protocol:
Cells were harvested and total RNA was extracted by using RNAmini kit (Qiagen, Germany). 1 μg of total RNA was used for the construction of sequencing libraries.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

value: spleen

value: primary culture cell

value: CD8+T cell

value: C57 BL/6 wt

value: ABCT Buffer


title: A375_GL2-T-3_R1

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
We prepared QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, LEX113.96) libraries from RNA following the manufacturer’s instructions. 500ng of RNA were spiked-in with 1µL of a 1:100 dilution of ERCC Spike-In Mix (ThermoFisher, 4456740) before the library preparation. Libraries were then quantified, pooled and sent for sequencing at Novogene (Novaseq 6000 2x150)

value: skin melanoma

value: siRNA targetting GL2 for 42h followed by tryptolide treatment for 3 hours


title: A375_CTU2-TCHX-0_R3

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 0 hours


title: S2KO rep1

description:
S2KO_merged_nodups.txt.gz
S2KO_inter_30.hic

value: knockout silencer2 region


title: Perio 4


title: L_4F_3


title: S1KO H3K27ac rep1

value: knockout silencer1 region


title: Perio 3

value: chronic pariodontiits


title: L_4F_2


title: ABCT_Buffer_1


title: S1KO rep2

description:
S1KO_merged_nodups.txt.gz
S1KO_inter_30.hic


title: Healthy  2

value: Healthy


title: A375_CTU2-T-3_R3

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 3 hours


title: Skin, DPCP, rep3

city: Taipei

first: Kai-Rong

last: Huang

address: No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan

department: Biomedical Engineering

country: Taiwan

institute: National Taiwan University

data_processing:
The quality of the raw reads was checked using fastq.gzC (v0.11.9).
The raw reads were checked with fastq.gzC (v0.11.9) and trimmed using Trimmomatic (v0.36).
The clean reads were aligned to the reference genome using HISAT2 (v2.2.1).
StringTie (v2.2.1) was used to do read count normalization. FeatureCounts (v1.6.2) was used to do reads summarization.
Differential expression analysis was conducted with either DEGseq (v1.48.0) without biological replicates or DESeq2 (v1.34.0) with biological replicates.
Assembly: mm10
Supplementary files format and content: tab-limited text file incluides raw counts for each sample
Supplementary files format and content: xlsx file for normalized read count

source_name: Skin

extract_protocol:
Fresh dorsal skin tissue was cut into small pieces and stabilized by RNAlater™ Stabilization Solution (Thermo Fisher Scientific) overnight at 4°C. RNA was isolated using TRIzol™ Reagent (Invitrogen).
Library construction for all samples utilized the Illumina TruSeq Stranded mRNA kit for 150 bp paired-end sequencing on the NovaSeq 6000 platform.

value: Skin

value: DPCP


title: S1KO rep1

value: Arima


title: A375_CTU2-T-0_R3

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 0 hours


title: Wildtype control, five days old lens 2

value: Lens

value: FVB/N


title: A375_GL2-TCHX-0_R1

value: siRNA targetting GL2 for 42h followed by cycloheximid and tryptolide treatment for 0 hours


title: L_4F_1

value: spleen

value: primary culture cell

value: CD8+T cell

value: C57 BL/6 wt


title: Healthy  1

value: gingiva tissues


title: ABCT_Buffer_2

value: ABCT Buffer


title: DKO rep1

value: knockout silencer1 and 2 regions


title: YUCHIME_siITGA3_3_S6

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

data_processing:
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Homo sapien sapien hg38.
Assembly: Human hg38
Supplementary files format and content: SALMON - format - .sf - TMM and read counts

source_name: metatastic melanoma cells

growth_protocol: Primary melanocytes were grown in melanocyte growth media. WM35, 983, 902, and 1552 cell lines were grown in 2% tumor media. YUPEET and YUCHIME cell lines were grown in basic FGF media.

extract_protocol:
Cells were pelleted and RNA was harvested using the Qiagen Rneasy kit. Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (for removal of rRNA) (Cat#20020598) was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: metatastic melanoma cells

tag: gender

value: M

tag: cohort

value: Wistar

tag: genotype/variation

value: siRNA ITGA3


title: A375_CTU2-TCHX-3_R2

value: skin melanoma

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 3 hours


title: YUCHIME_siITGA3_2_S5


title: combined 24H rep2

description:
24H_combined_merged_nodups.txt.gz
24H_combined_inter_30.hic

source_name: K562 cells with combination of GSK343 and X5050 for 24h

value: Arima

value: treated with GSK343 and X5050 for 24 hours


title: YUCHIME_siITGA3_1_S4


title: Perio 1

value: chronic pariodontiits


title: combined 24H rep1


title: S2KO rep2

value: knockout silencer2 region


title: YUCHIME_siControl3_S3

value: siRNA scramble


title: A375_CTU2-T-3_R2

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 3 hours


title: Healthy  4

value: Healthy


title: combined 8H rep1

description:
8H_combined_merged_nodups.txt.gz
8H_combined_inter_30.hic

source_name: K562 cells with combination of GSK343 and X5050 for 8h

value: treated with GSK343 and X5050 for 8 hours


title: A375_CTU2-T-5_R3

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 5 hours


title: Skin, DPCP+Encapsome, rep2

value: Skin

value: DPCP+Encapsome


title: Perio 2

value: gingiva tissues


title: A375_CTU2-TCHX-5_R3

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 5 hours


title: A375_CTU2-TCHX-5_R1


title: Skin, DPCP, rep2

value: DPCP


title: EV rep2

description:
EV_merged_nodups.txt.gz
EV_inter_30.hic

source_name: K562 cells with empty vector

value: untreated


title: Skin, DPCP, rep1


title: Healthy  3


title: Skin, DPCP+Encapsome, rep1


title: Skin, control, rep1

value: control


title: EV rep1

description:
EV_merged_nodups.txt.gz
EV_inter_30.hic


title: Skin, control, rep3


title: Skin, control, rep2


title: A375_CTU2-TCHX-0_R1

value: skin melanoma

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 0 hours


title: X5050 rep2

description:
X5050_merged_nodups.txt.gz
X5050_inter_30.hic

value: Arima

value: treated with100µm X5050 for  72hours


title: A375_CTU2-T-5_R2


title: YUCHIME_siControl2_S2

value: metatastic melanoma cells

value: M

value: Wistar


title: combined 8H rep2


title: A375_CTU2-TCHX-5_R2


title: Skin, DPCP+Codrosome, rep2

value: DPCP+Codrosome


title: SKMel147_siITGA3_1_S10

value: siRNA ITGA3


title: A375_CTU2-T-0_R2

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 0 hours


title: combined 72H rep1

description:
72H_combined_merged_nodups.txt.gz
72H_combined_inter_30.hic

value: treated with GSK343 and X5050 for 72 hours


title: SKMel147_siControl2_S8

value: siRNA scramble


title: YUCHIME_siControl1_S1


title: A375_CTU2-TCHX-0_R2


title: combined 72H rep2


title: Skin, DPCP+Encapsome, rep3

value: Skin

value: DPCP+Encapsome


title: Skin, DPCP+Codrosome, rep3


title: CByB6F1 RUX-treated-6

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description:
XF-8621-6
readcounts.txt

data_processing:
Paired-end reads were aligned to the reference genome mm10 using STAR
featureCounts was used to count the reads numbers mapped to each gene with UCSC annotation.
Assembly: mm10
Supplementary files format and content: readcounts.txt

source_name: Mouse Bone Marrow

extract_protocol: Libraries were generted using SMART-Seq mRNA LP Kit (Takara).

value: Female

tag: age

value: 2-5 months

tag: subject

value: RUX-treated

value: bone marrow


title: CByB6F1 RUX-treated-5

description:
XF-8621-5
readcounts.txt

tag: Sex


title: DMSO rep2

description:
DMSO_merged_nodups.txt.gz
DMSO_inter_30.hic

value: untreated


title: SKMel147_siITGA3_3_S12


title: A375_CTU2-T-0_R1

first: Nicolas

last: Fontrodona

address: 46 allée d'Italie

institute: ENS de Lyon

value: skin melanoma


title: X5050 rep1

source_name: K562 cells with X5050

value: Arima

value: treated with100µm X5050 for  72hours


title: DMSO rep1


title: A375_CTU2-T-5_R1

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 5 hours


title: Skin, DPCP+Codrosome, rep1


title: A375_DMSO-TCHX-5_R2

data_processing:
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 20 -3 --cut_tail_window_size 10 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA –adapter_sequence=AAAAAA)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10  -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
We prepared QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, LEX113.96) libraries from RNA samples following the manufacturer’s instructions. 500ng of RNA were spiked-in with 1µL of a 1:100 dilution of ERCC Spike-In Mix (ThermoFisher, 4456740) before the library preparation. Libraries were then quantified, pooled and sent for sequencing at Novogene (Novaseq 6000 1x150)

treatment_protocol: Cells were plated and the following day, the culture medium was removed and replaced with fresh medium containing 1µM vemurafenib and cobimetinib (500nM vemurafenib + 500nM cobimetinib) or DMSO. 18h later, cells were treated with fresh cycloheximid (100µg/ml) or DMSO. 5 minutes later, cells were treated with tryptolide (25µM) or DMSO, making a total of 2x2x2 = 8 samples so far. This was prepared in 4 identical batches A B C D, and batch A was immediately harvested after +/- tryptolide treatment (T0 samples). Batches B, C and D were harvested 1h, 3h and 5h later, respectively (samples T1, T3 and T5).

value: DMSO followed by cycloheximid and tryptolide treatment for 5 hours


title: YUCHIME_2

data_processing:
Reads were aligned and counts called using STAR.
DEseq2 was used to normalize expression counts and perform DEG analysis.
 GSEA was performed for each comparison against all HALLMARK and Curated-Canonical pathways from the MSigDB.

source_name: Primary melanoma cells

value: M

tag: age at diagnosis

value: Yale

value: Primary melanoma cells


title: GSK343 rep2

description:
GSK343_merged_nodups.txt.gz
GSK343_inter_30.hic

value: treated with 5µm GSK343 for 72hours


title: A375_CTU2-T-3_R1

value: siRNA targetting CTU2 for 42h followed by tryptolide treatment for 3 hours


title: A375_CTU2-TCHX-3_R1

value: siRNA targetting CTU2 for 42h followed by cycloheximid and tryptolide treatment for 3 hours


title: SKMel147_siITGA3_2_S11

value: metatastic melanoma cells

value: siRNA ITGA3


title: A375_DMSO-TCHX-5_R1


title: mouse lung, wild type + Aspergillus, Sample 20

first: Kirk

middle: M.

last: Druey

address: 10 Center Drive Room 11N238A

department: NIAID

data_processing:
Adapter and quality trimmed using CutAdapt v1.18
Trimmed reads were mapped to GRCh38 reference and GENCODE v39 using STAR v2.7.6a in 2pass mode
Gene-level expression quantification was performed using RSEM v.1.3.0
Assembly: GRCm38, GENCODE M25
Supplementary files format and content: text, matrix of CPM and TMM normalized counts

source_name: Lung

extract_protocol:
Qiagen RNEasy
Illumina Truseq mRNA Prep Kit

tag: tissue

value: Lung

value: Balb/cJ

value: WT

value: Aspergillus funigatus


title: GSK343 rep1


title: CByB6F1 RUX-treated-4

description:
XF-8621-4
readcounts.txt

value: Female

value: 2-5 months

value: RUX-treated

value: bone marrow


title: SKMel147_siControl3_S9

value: siRNA scramble


title: CByB6F1 normal-3

description:
XF-8621-3
readcounts.txt

value: untreated


title: YUCHIME_1

value: M

value: Yale


title: mouse lung, wild type + Aspergillus, Sample 18


title: A375_DMSO-TCHX-3_R3

value: skin melanoma

value: DMSO followed by cycloheximid and tryptolide treatment for 3 hours


title: mouse lung, wild type + Aspergillus, Sample 19


title: CByB6F1 normal-2

description:
XF-8621-2
readcounts.txt


title: WM1552_3

value: Wistar

value: Primary melanoma cells


title: SKMel147_siControl1_S7

value: metatastic melanoma cells


title: WM1552_2


title: A375_DMSO-TCHX-1_R3

value: DMSO followed by cycloheximid and tryptolide treatment for 1 hours


title: A375_DMSO-TCHX-5_R3

value: DMSO followed by cycloheximid and tryptolide treatment for 5 hours


title: CByB6F1 normal-1

description:
XF-8621-1
readcounts.txt


title: CByB6F1 BMF RUX+CSA-treated-23

description:
XF-8569-23
readcounts.txt

value: RUX+CSA-treated


title: WM1552_1


title: CByB6F1 BMF RUX+CSA-treated-24

description:
XF-8569-24
readcounts.txt


title: A375_DMSO-TCHX-3_R1


title: YUCHIME_3


title: mouse lung, wild type + PBS, Sample 15

value: Lung

value: Balb/cJ

value: WT

value: PBS


title: WM902_2


title: CByB6F1 BMF RUX-treated-21

description:
XF-8569-21
readcounts.txt

value: Female

value: 2-5 months

value: RUX-treated

value: bone marrow


title: A375_DMSO-TCHX-1_R1


title: mouse lung, wild type + PBS, Sample 16


title: CByB6F1 BMF RUX+CSA-treated-22

description:
XF-8569-22
readcounts.txt


title: A375_DMSO-TCHX-1_R2


title: WM902_3

value: M


title: A375_DMSO-TCHX-3_R2

value: skin melanoma


title: mouse lung, RGS4 knockout + Aspergillus, Sample 14

value: RGS4 KO

value: Aspergillus funigatus


title: mouse lung, RGS4 knockout + Aspergillus, Sample 13


title: CByB6F1 BMF RUX-treated-19

description:
XF-8569-19
readcounts.txt


title: A375_DMSO-TCHX-0_R2

value: DMSO followed by cycloheximid and tryptolide treatment for 0 hours


title: CByB6F1 BMF CSA-treated-18

description:
XF-8569-18
readcounts.txt

value: CSA-treated


title: WM983_2

value: Wistar

value: Primary melanoma cells


title: mouse lung, RGS4 knockout + PBS, Sample 11


title: WM902_1


title: CByB6F1 BMF RUX-treated-20

description:
XF-8569-20
readcounts.txt


title: mouse lung, wild type + PBS, Sample 17


title: A375_DMSO-TCHX-0_R3


title: mouse lung, RGS4 knockout + Aspergillus, Sample 12


title: WM983_3


title: CByB6F1 BMF CSA-treated-17

description:
XF-8569-17
readcounts.txt


title: WM983_1


title: A375_DMSO-T-5_R3

value: DMSO followed by tryptolide treatment for 5 hours


title: A375_DMSO-TCHX-0_R1


title: A375_DMSO-T-5_R1


title: BHLKO_3

first: Vaishnavi

last: Dandavate

address: 26B Arthur Ruppin street

department: Biomolecular Sciences

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample
Normalization of the counts and differential expression analysis was performed using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (DOI:10.1111/j.2517-6161.1995.tb02031.x).
Assembly: mm10
Supplementary files format and content: xlsx files containing the raw counts and normalized counts for each gene and sample

growth_protocol: 3-5 months old mice were housed under standard light-dark conditions (12h/12h) for 2 weeks before the experiment, till the day of the experiment.

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissection and stored at -80°C till used. For RNA extraction, the tissues were soaked in TRI-reagent (Sigma) and were homogenized by bead beater (Bead Ruptor e24, OMNI), and then proceeded by a standard TRI-reagent based RNA extraction protocol. RNA concentration was determined using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific). RNA Integrity was validated using 2200 TapeStation (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lights were turned off at the transition of dark to light regiment on the day of the experiment following regular LD regimen, food served ad libitum

value: Lung

tag: strain

tag: ct

value: Alb-Cre+ Hif1_alpha fl/fl Bmal1fl/fl


title: mouse lung, RGS4 knockout + PBS, Sample 10

tag: cell line

value: Balb/cJ

tag: treatment


title: WM35_3

value: F

tag: cell type


title: CByB6F1 BMF CSA-treated-16

description:
XF-8569-16
readcounts.txt

value: Female


title: mouse lung, RGS4 knockout + PBS, Sample 9

value: PBS


title: A375_DMSO-T-5_R2


title: CByB6F1 BMF untreated-15

description:
XF-8569-15
readcounts.txt

value: 2-5 months

value: untreated


title: BHLKO_4


title: YUPEET_1

value: M

value: Yale


title: YUPEET_2


title: CByB6F1 BMF untreated-14

description:
XF-8569-14
readcounts.txt

value: bone marrow


title: WM35_1


title: A375_DMSO-T-3_R3

value: skin melanoma

value: DMSO followed by tryptolide treatment for 3 hours


title: CByB6F1 BMF untreated-13

description:
XF-8569-13
readcounts.txt


title: Human Epi Melanocytes_3

source_name: Primary Melanocytes

value: not applicable

value: Primary Melanocytes


title: BHLKO_2


title: CByB6F1 BMF RUX+CSA-treated-10

description:
XF-8569-10
readcounts.txt

value: RUX+CSA-treated


title: YUPEET_3

value: Primary melanoma cells


title: WM35_2

value: Wistar


title: A375_DMSO-T-3_R2


title: CByB6F1 BMF RUX+CSA-treated-12

description:
XF-8569-12
readcounts.txt


title: CByB6F1 BMF RUX+CSA-treated-11

description:
XF-8569-11
readcounts.txt


title: BHLKO_1

value: Lung

value: Alb-Cre+ Hif1_alpha fl/fl Bmal1fl/fl


title: A375_DMSO-T-3_R1


title: A375_DMSO-T-1_R2

value: DMSO followed by tryptolide treatment for 1 hours


title: Human Epi Melanocytes_2


title: Alb-CRE_4

value: Alb-Cre


title: IVN Primary MCS_3


title: A375_DMSO-T-1_R3


title: FLT3_HIV_VX_rep3

city: Galveston

first: Steven

middle: G

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

description: polyA RNA-Seq

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A combined genome index was built with STAR (v2.7.9a) using the mouse GRCm39 and human GRCh38 genomes.
RNA-Seq reads were aligned to the combined  reference using the STAR software version 2.7.9a with the parameters recommended for the ENCODE consortium.
Human gene read counts were obtained from the STAR quantMode GeneCounts feature using the Gencode v38 annotation file.
Assembly: GRCm39 and GRCh38
Supplementary files format and content: Tab delimited table of raw gene read counts per sample.

source_name: Spleen

extract_protocol:
Poly-A plus RNA was enriched from ~0.1ug of total RNA and used to generate libraries using New England Biolabs NEBNext Ultra II Kit.
Bio-Rad Aurum™ Total RNA Mini Kit  following manufacturer's protocol
PolyA+ RNA was isolated and libraries were made with the New England BioLab NEBNext Ultra II RNA library kit.

value: Spleen

value: NOD/SCID/[gamma]cnil/nil

value: female

value: Adult

value: rFLT-3L+HIV+VX 765


title: Alb-CRE_3


title: CByB6F1 BMF RUX-treated-9

description:
XF-8569-9
readcounts.txt

value: Female

value: 2-5 months

value: RUX-treated

value: bone marrow


title: CByB6F1 BMF CSA-treated-6

description:
XF-8569-6
readcounts.txt

value: CSA-treated


title: FLT3_HIV_VX_rep2

description: polyA RNA-Seq


title: A375_DMSO-T-1_R1

city: Lyon

value: skin melanoma


title: Alb-CRE_2


title: A375_DMSO-T-0_R3

value: DMSO followed by tryptolide treatment for 0 hours


title: Alb-CRE_1


title: CByB6F1 BMF RUX-treated-7

description:
XF-8569-7
readcounts.txt


title: CByB6F1 BMF RUX-treated-8

description:
XF-8569-8
readcounts.txt


title: A375_DMSO-T-0_R2


title: A375_DMSO-T-0_R1


title: YUCHIME_Input

data_processing:
Reads were aligned to the human reference genome hg19 using Bowtie v1.1.2 (Langmead et al., 2009) with parameters –l 40 –n 2 –best –k 1 –m 1, and read quality was assessed using fastQC (Simon Andrews, 2019).
Duplicate reads were removed with PICARD v2.2.4 (Broad Institute)
Binary alignment maps (BAM) files were generated with samtools v1.9 (Li et al., 2009) which were used in downstream analysis. MACS2 v2.1.0 (Zhang et al., 2008) was used to call significant peaks (For H3K27ac: q < 1e-11).
Peaks within ENCODE blacklisted regions were removed. Coverage tracks were generated from BAM files using deepTools 3.2.1 (Ramírez et al., 2016) bamCoverage with parameters –scaleFactor X and –binsize 10.
The normalization scale factor was calculated for each sample based on the Drosophila de-duplicated uniquely aligned reads as previously described (Egan et al., 2016).
Genome_build: Human genome hg10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27Ac antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S).     Libraries were sequenced on Illumina's NextSeq500 following the manufacturer's protocols.

value: Primary melanoma cells

tag: chip antibody


title: FLT3_HIV_rep3

description: polyA RNA-Seq


title: A375_DMSO-DMSO-5_R2

value: DMSO followed by DMSO treatment for 5 hours


title: Human Epi Melanocytes_1

value: not applicable

value: Primary Melanocytes


title: IVN Primary MCS_2


title: IVN Primary MCS_1


title: CByB6F1 BMF untreated-2

description:
XF-8569-2
readcounts.txt

value: untreated


title: FLT3_HIV_VX_rep1

description: polyA RNA-Seq

value: Spleen


title: CByB6F1 BMF CSA-treated-5

description:
XF-8569-5
readcounts.txt


title: CByB6F1 BMF CSA-treated-4

description:
XF-8569-4
readcounts.txt


title: FLT3_HIV_rep2

description: polyA RNA-Seq

value: NOD/SCID/[gamma]cnil/nil


title: FLT3_HIV_rep1

description: polyA RNA-Seq

value: female


title: YUPEET_Input


title: A375_DMSO-DMSO-5_R3


title: WM35_Input


title: CByB6F1 BMF untreated-1

description:
XF-8569-1
readcounts.txt


title: FLT3_rep3

description: polyA RNA-Seq

value: Adult


title: A375_DMSO-DMSO-5_R1


title: WM1552_Input


title: A375_DMSO-DMSO-3_R2

value: DMSO followed by DMSO treatment for 3 hours


title: YUPEET_H3K27Ac

value: H3K27Ac (EpiCypher 13-0045)


title: A375_DMSO-DMSO-3_R1


title: A375_DMSO-DMSO-3_R3


title: WM1552_H3K27Ac


title: P0, scRNAseq

city: Guangzhou

first: Yingying

last: Xiao

address: A2-652, Guangzhou Medical University, Xinzao Road, Panyu District, Guangzhou

institute: Guangzhou Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Ensembl release 104 for Mus musculus
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
For P0 sample, freshly collected cells from the heart region of E9.5 mouse embryos were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2 for three times. The tissue was were cut into small pieces and resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 15 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). For P6 sample, cells were digested by accutase, and then washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: heart

value: tissue

value: heart cell

tag: genotype

value: C57BL/6 mice embryos

value: isolated and then sequenced


title: YUCHIME_H3K27Ac


title: FLT3_rep2

description: polyA RNA-Seq


title: P6, scRNAseq

description: 10x Genomics

value: isolated, cultured and then sequenced


title: WM35_H3K27Ac

value: Primary melanoma cells


title: Horse 24, immune, d18pi

city: Ithaca

first: Bettina

last: Wagner

address: 240 Farrier Drive

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

description:
NE56-Horse24-D18pi
equine_rawCounts.txt

data_processing:
Initial processing was carried out Cornell University’s Transcriptional Regulation and Expression (TREx) facility
Reads were trimmed for loq quality and adaptor sequences using TrimGalor v0.6.0, cutadapt, and fastQC.
Equine sequences were aligned using STAR v2.7.0e, to generate a raw counts table.
SARTools and DESeq2 v1.26.0 was used to generate normalized counts and statistical analysis of differential gene expression. Raw counts were additionally analyzed in iDEP.951, to determine differential expression
Viral sequences were aligned to the EHV-1 Ab4 genome (NC_001491.2) and a raw counts table was generated usinghtseq-count (Galaxy Version 0.9.1)
Assembly: EquCab 2.0
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Equus caballus

source_name: nasal mucosa

extract_protocol:
RNA was extracted using TRIzol LS reagent (Life Technologies Corporation, Carlsbad, CA, USA) following the manufacturer’s protocol.
RNA was processed using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) to create a cDNA library, which was quantified with a Qubit 2.0 (dsDNA HS Kit, Thermo Fisher, Waltham, MA, USA) and fragment size distribution was determined by Fragment Analyzer (Advanced Analytical, Orangeburg, NY, USA).

treatment_protocol: All horses were intranasally infected with 1x10^7 PFU neuropathogenic EHV-1 Ab4 on d0.

value: nasal mucosa

value: EHV-1 Ab4 challenge

tag: time

tag: immune status

value: immune

tag: breed

value: Icelandic


title: FLT3_rep1

description: polyA RNA-Seq

value: Spleen


title: A375_DMSO-DMSO-1_R3

value: skin melanoma

value: DMSO followed by DMSO treatment for 1 hours


title: CByB6F1 BMF untreated-3

description:
XF-8569-3
readcounts.txt

value: Female

value: 2-5 months

value: untreated

value: bone marrow


title: WT non-treated control 3

city: San Diego

first: Paulo

middle: VG

last: Alabarse

address: 9500 Gilman Drive

department: Rheumatology

institute: University of California, San Diego

data_processing:
Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie
Assembly: All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Supplementary files format and content: Excel file include FPKM values for each sample

source_name: Bone marrow derived macrophages

growth_protocol: Isolated mouse bone marrows were cultured in RPMI containing 10% FBS, penicillin (100 U/ml), streptomycin (100 μg/ml) and 20% L929 conditioned media for 7 days. After priming with GM-CSF (20 ng/ml) for 24 hours, cells were washed with PBS and subjected to experiments in RPMI containing 1% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA samples were sent to LC sciences for RNA-seq
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library was then constructed.

treatment_protocol: WT BMDMs in the presence or absence of apigenin (25 uM) and CD38KO BMDMs were stimulated with MSU crystals (0.2 mg/ml) for 6 hours.

value: Bone marrow derived macrophages

value: WT


title: Horse 20, non-immune, d18pi

description:
NE55-Horse20-D18Pi
equine_rawCounts.txt

value: non-immune


title: A375_DMSO-DMSO-1_R2